Rewashing the spotted negatives seems to have worked pretty well. I may have added a scratch or two in the process so I'll be more gentle in the future. I simply dropped the cut negative into a dish with Stabilizer and swished everything around for a minute or so, then carefully (but not carefully enough) ran a damp sponge along each of them.
I may try longer washes next time per BMbikerider's recommendation. Overall I'm finding C-41 development to be much easier than expected, and the results (besides the above issues) have been very encouraging. Being able to process Portra 400 in 120 without having to ship it somewhere is terrific, and a _lot_ less expensive.